RetrogeneDB ID: retro_tbel_3708

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148981:68497..69217(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSTBEG00000002066
• Aliases: None
• Description: chaperonin containing TCP1, subunit 7 (eta) [Source:HGNC Symbol;Acc:1622]

Sequence

>retro_tbel_3708
CCCACACCAGTTATACTGTTGAAAGAGGGAACTGATAGCTCTCAAGGCATCCCCCAACTTGTGAGTAATATTTGTGCCTG
CCAGGTGATTGCTAAGGCTGTAAGAACCACCCTCGGTCCCCATGGCATGGACAAGCTAATTGTGGATAGCCAAGGCAAAG
CAACTATTTCTAATGATGGGGCCACAATTCTGAAACTCCTTGATGTCGTCCATACTGCAGCAAAGACTTTAGTGGACATT
GCCAAATCCCAAGATGCTGAGATTGGTGATGGCACCACCTCTGTGACCCTGCTGGCTGCAGGGTTCCTGAAGCAGGTGGA
ACCATATGTGGAGGAAGGTTTGCACCCGCAGATCATCATTCAAGCTTTCCGCACAGCCACTCAGTTGGTAGTTAACAAGA
TCAGAGAGATTGCTGTGACCATGAAGAAGCAAGATAAGGTGGAACAGAGGAAGCTGCTGGAGAAATGTGCCATGACAGCG
CTGAGCTCCAAGCTGAGCTCCCAACAGAAAGCTTTCTTTGCCAAGATGGTGGTGGATGCGGTGATGATGCTCGATGACTT
GCTCCAGCTTAAAATGATTCGAATCAAGAAGATTCAGGGTGGAGCCCTAGAGGAGTCTCAACTGGTTGTTGGTAATGCAT
TCAAGAAGACCTTCTCTTACGCTGAGTTTGAAATGCAGCGCAAAAAGTACAGTAATCCCAGGATTGCCCTTTTGAATATG

Alignment

ORF - retro_tbel_3708 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.25 %
• Parental protein coverage: 51.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVV
          PTPVILLKEGTDSSQGIPQLVSNI.ACQVIA.AVRTTLGP.GMDKLIVD..GKATISNDGATILKLLDVV
Retrocopy PTPVILLKEGTDSSQGIPQLVSNICACQVIAKAVRTTLGPHGMDKLIVDSQGKATISNDGATILKLLDVV

Parental  HPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNKIREIAVT
          H.AAKTLVDIAKSQDAE.GDGTTSVTLLAA.FLKQV.PYVEEGLHPQIII.AFRTATQL.VNKIREIAVT
Retrocopy HTAAKTLVDIAKSQDAEIGDGTTSVTLLAAGFLKQVEPYVEEGLHPQIIIQAFRTATQLVVNKIREIAVT

Parental  VKKQDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGALEESQLVA
          .KKQDKVEQRKLLEKCAMTALSSKL.SQQKAFFAKMVVDAVMMLDDLLQLKMI.IKK.QGGALEESQLV.
Retrocopy MKKQDKVEQRKLLEKCAMTALSSKLSSQQKAFFAKMVVDAVMMLDDLLQLKMIRIKKIQGGALEESQLVV

Parental  GVAFKKTFSYAGFEMQPKKYSNPKIALLNV
          G.AFKKTFSYA.FEMQ.KKYSNP.IALLN.
Retrocopy GNAFKKTFSYAEFEMQRKKYSNPRIALLNM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3708 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3708 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Choloepus hoffmanni	ENSCHOG00000007937	1 retrocopy	retro_chof_2313,
Cavia porcellus	ENSCPOG00000019869	1 retrocopy	retro_cpor_1458,
Echinops telfairi	ENSETEG00000009409	2 retrocopies	retro_etel_1478, retro_etel_607,
Homo sapiens	ENSG00000135624	1 retrocopy	retro_hsap_3354,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Nomascus leucogenys	ENSNLEG00000010414	1 retrocopy	retro_nleu_1175,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Pongo abelii	ENSPPYG00000012297	1 retrocopy	retro_pabe_2760,
Pan troglodytes	ENSPTRG00000012060	1 retrocopy	retro_ptro_2133,
Rattus norvegicus	ENSRNOG00000015630	2 retrocopies	retro_rnor_2179, retro_rnor_535,
Sorex araneus	ENSSARG00000011475	1 retrocopy	retro_sara_539,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708 , retro_tbel_3751,